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The flyways of many different wild waterfowl pass through the Caspian Sea region. The western coast of the middle Caspian Sea is an area with many wetlands, where wintering grounds with large concentrations of birds are located. It is known that wild waterfowl are a natural reservoir of the influenza A virus. In the mid-2000s, in the north of this region, the mass deaths of swans, gulls, and pelicans from high pathogenicity avian influenza virus (HPAIV) were noted. At present, there is still little known about the presence of avian influenza virus (AIVs) and different avian paramyxoviruses (APMVs) in the region's waterfowl bird populations. Here, we report the results of monitoring these viruses in the wild waterfowl of the western coast of the middle Caspian Sea from 2017 to 2020. Samples from 1438 individuals of 26 bird species of 7 orders were collected, from which 21 strains of AIV were isolated, amounting to a 1.46% isolation rate of the total number of samples analyzed (none of these birds exhibited external signs of disease). The following subtypes were determined and whole-genome nucleotide sequences of the isolated strains were obtained: H1N1 ( n = 2), H3N8 ( n = 8), H4N6 ( n = 2), H7N3 ( n = 2), H8N4 ( n = 1), H10N5 ( n = 1), and H12N5 ( n = 1). No high pathogenicity influenza virus H5 subtype was detected. Phylogenetic analysis of AIV genomes did not reveal any specific pattern for viruses in the Caspian Sea region, showing that all segments belong to the Eurasian clades of classic avian-like influenza viruses. We also did not find the amino acid substitutions in the polymerase complex (PA, PB1, and PB2) that are critical for the increase in virulence or adaptation to mammals. In total, 23 hemagglutinating viruses not related to influenza A virus were also isolated, of which 15 belonged to avian paramyxoviruses. We were able to sequence 12 avian paramyxoviruses of three species, as follows: Newcastle disease virus ( n = 4); Avian paramyxovirus 4 ( n = 5); and Avian paramyxovirus 6 ( n = 3). In the Russian Federation, the Newcastle disease virus of the VII.1.1 sub-genotype was first isolated from a wild bird (common pheasant) in the Caspian Sea region. The five avian paramyxovirus 4 isolates obtained belonged to the common clade in Genotype I, whereas phylogenetic analysis of three isolates of Avian paramyxovirus 6 showed that two isolates, isolated in 2017, belonged to Genotype I and that an isolate identified in 2020 belonged to Genotype II. The continued regular monitoring of AIVs and APMVs, the obtaining of data on the biological properties of isolated strains, and the accumulation of information on virus host species will allow for the adequate planning of epidemiological measures, suggest the most likely routes of spread of the virus, and assist in the prediction of the introduction of the viruses in the western coastal region of the middle Caspian Sea., Competing Interests: The authors declare no conflicts of interest. The funding entities had no role in the design of the study, in the collection of material, analyses or interpretation of data, in the writing of the manuscript, or in the decision to publish the results.

The black-necked crane (Grus nigricollis) is a vulnerable species, breeding exclusively on the high-altitude wetlands of the Qinghai-Tibet Plateau. Bird species harbor diverse communities of microorganisms within their gastrointestinal tracts, which have important roles in the health, nutrition, and physiology of birds. Hitherto, virtually nothing was known about the gut microbial communities associated with wild black-necked cranes. For the first time, this study characterized the gut microbial community compositions, diversity, and functions of black-necked cranes from six wintering areas in China using the Illumina Miseq platform. The taxonomic results revealed that Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the four most abundant phyla in the gut of black-necked cranes. At the genus level, 11 genera including Lactobacillus, Pseudomonas, Carnobacterium, Pantoea, Enterococcus, Erwinia, Turicibacter, Bacillus, Phenylobacterium, Sanguibacter, and Psychrobacter were dominant. The differences in the gut microbial community alpha and the beta diversities of black-necked cranes among the six wintering areas were investigated. Furthermore, the representative microbial taxa and their predicted functions in each wintering location were also determined. These data represent the first analysis of the gut microbiome of black-necked cranes, providing a baseline for further microbiological studies and a foundation for the conservation of this bird.

An H5N6 highly pathogenic avian influenza virus (HPAIV) outbreak occurred in poultry in Japan during January 2018, and H5N6 HPAIVs killed several wild birds in 3 prefectures during Winter 2017-2018. Time-measured phylogenetic analyses demonstrated that the Hemagglutinin (HA) and internal genes of these isolates were genetically similar to clade 2.3.4.4.B H5N8 HPAIVs in Europe during Winter 2016-2017, and Neuraminidase (NA) genes of the poultry and wild bird isolates were gained through distinct reassortments with AIVs that were estimated to have circulated possibly in Siberia during Summer 2017 and Summer 2016, respectively. Lethal infectious dose to chickens was similar between the poultry and wild-bird isolates. H5N6 HPAIVs during Winter 2017-2018 in Japan had higher 50% chicken lethal doses and lower transmission efficiency than the H5Nx HPAIVs that caused previous outbreaks in Japan, thus explaining in part why cases during the 2017-2018 outbreak were sporadic., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Genetically related highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype caused outbreaks simultaneously in East Asia and Europe-geographically distinct regions-during winter 2017-2018. This situation prompted us to consider whether the application of phylogeographic analysis to a particular gene segment of AIVs could provide clues for understanding how AIV had been disseminated across the continent. Here, the N6 NA genes of influenza viruses isolated across the world were subjected to phylogeographic analysis to illustrate the inter- and intracontinental dissemination of AIVs. Those isolated in East Asia during winter and in Mongolia/Siberia during summer were comingled within particular clades of the phylogeographic tree. For AIVs in one clade, their dissemination in eastern Eurasia extended from Yakutia, Russia, in the north to East Asia in the south. AIVs in western Asia, Europe, and Mongolia were also comingled within other clades, indicating that Mongolia/Siberia plays an important role in the dissemination of AIVs across the Eurasian continent. Mongolia/Siberia may therefore have played a role in the simultaneous outbreaks of H5N6 HPAIVs in Europe and East Asia during the winter of 2017-2018. In addition to the long-distance intracontinental disseminations described above, intercontinental disseminations of AIVs between Eurasia and Africa and between Eurasia and North America were also observed. Integrating these results and known migration flyways suggested that the migration of wild birds and the overlap of flyways, such as that observed in Mongolia/Siberia and along the Alaskan Peninsula, contributed to the long-distance intra- and intercontinental dissemination of AIVs. These findings highlight the importance of understanding the movement of migratory birds and the dynamics of AIVs in breeding areas-especially where several migration flyways overlap-in forecasting outbreaks caused by HPAIVs., Competing Interests: The authors have declared that no competing interests exist.

The emergence of novel avian influenza viruses in migratory birds is of concern because of the potential for virus dissemination during fall migration. We report the identification of novel highly pathogenic avian influenza viruses of subtype H5N8, clade 2.3.4.4, and their reassortment with other avian influenza viruses in waterfowl and shorebirds of Siberia.

Wild waterfowl undertake a variety of long-distance flights during their migration. These flights provide birds with the opportunities to both acquire and disseminate avian influenza viruses (AIVs). The Asian portion of Russia is crossed by four major migration routes and represents the major breeding area for many wild bird species in the Palearctic. The Asian territory of Russia plays an important role in distribution, persistence, and evolution of AIVs due to the ecologic relationships of bird populations from Russia and different Asian, European, African, and North American countries. Our study highlights the results of surveillance conducted in 2008 for AIVs in wild birds in the Asian portion of Russia. During this study, our team collected and tested 5678 samples from wild birds. Among them, 41 samples tested positive for AIV with an isolation rate of 0.72%. The highest AIV prevalence, 1.49%, was found in Anseriformes. In Ardeidae and Laridae, the AIV prevalence was 1.23% and 0.64%, respectively. Rallidae showed the lowest AIV prevalence of 0.61%. Phylogenetic analysis of H3 and H4 subtypes represented close relationships of AIVs isolated from the Asian portion of Russia to the AI strains from Asia, Africa, and Europe. These findings were confirmed by the wild bird migration routes that affect bird populations from Eurasian, African, Australian, and North American continents.

The coastal and estuarine wetlands of the northern Caspian Sea, which borders southeast Russia, provide support for millions of waterfowl and shorebirds during nesting, molting, migration, and wintering periods (1,2); [...]

Metabolomics is a powerful set of methods that uses analytical techniques to identify and quantify metabolites in biological samples, providing a snapshot of the metabolic state of a biological system. In medicine, metabolomics may help to reveal the molecular basis of a disease, make a diagnosis, and monitor treatment responses, while in agriculture, it can improve crop yields and plant breeding. However, animal metabolomics faces several challenges due to the complexity and diversity of animal metabolomes, the lack of standardized protocols, and the difficulty in interpreting metabolomic data. The current dataset includes quantitative metabolomic profiles of eye lenses from 26 bird species (111 specimens) that can aid researchers in developing new experiments, mathematical models, and integrating with other "-omics" data. The dataset includes raw 1H NMR spectra, protocols for sample preparation, and data preprocessing, with the final table containing information on the abundance of 89 reliably identified and quantified metabolites. The dataset is quantitative, making it relevant for supplementing with new specimens or comparison groups, followed by data mining and expected new interpretations. The data were obtained using the bird specimens collected in compliance with ethical standards and revealed potential differences in metabolic pathways due to phylogenetic differences or environmental exposure. Dataset: The dataset, including NMR raw data, metabolite concentrations, and experimental protocols, has been deposited in the MetaboLights repository, study identifier MTBLS7739 (https://www.ebi.ac.uk/metabolights/MTBLS7739 (accessed on 30 June 2023)). DOI: 10.1093/nar/gkz1019, PMID: 31691833. This dataset is now also available through the laboratory's own database, accessible via the following links: amdb.online/amdb/experiments/145/; amdb.online/amdb/experiments/199/; amdb.online/amdb/experiments/255/; amdb.online/amdb/experiments/248/. Dataset License: CC0 [ABSTRACT FROM AUTHOR]

Simple Summary: Modern evolutionary biology offers a wide variety of methods to explore the evolution of species and to describe their relationships. The methods of DNA/RNA sequence analysis have been developing for decades and have become increasingly popular and reasonably reliable. Nevertheless, final phylogenetic trees for many taxa are still under debate because both classical and genomics-based approaches have their own limitations for phylogenetic tree reconstruction. Here, we propose the use of younger 'omics' methods, namely quantitative metabolomics, to aid the phylogeny reconstruction of vertebrates. We show that metabolomics-based hierarchical clustering analysis trees match, although not perfectly, to the genomics-based trees. In the current pilot study, we propose the use of quantitative metabolomics to reconstruct the phylogeny of vertebrates, namely birds. We determined the concentrations of the 67 most abundant metabolites in the eye lenses of the following 14 species from 6 orders of the class Aves (Birds): the Black kite (Milvus migrans), Eurasian magpie (Pica pica), Northern raven (Corvus corax), Eurasian coot (Fulica atra), Godlewski's bunting (Emberiza godlewskii), Great crested grebe (Podiceps cristatus), Great tit (Parus major), Hawfinch (Coccothraustes coccothraustes), Hooded crow (Corvus cornix), House sparrow (Passer domesticus), Rock dove (Columba livia), Rook (Corvus frugilegus), Short-eared owl (Asio flammeus) and Ural owl (Strix uralensis). Further analysis shows that the statistical approaches generally used in metabolomics can be applied for differentiation between species, and the most fruitful results were obtained with hierarchical clustering analysis (HCA). We observed the grouping of conspecific samples independently of the sampling place and date. The HCA tree structure supports the key role of genomics in the formation of the lens metabolome, but it also indicates the influence of the species lifestyle. A combination of genomics-based and metabolomics-based phylogeny could potentially resolve arising issues and yield a more reliable tree of life. [ABSTRACT FROM AUTHOR]

Since 2013, H5N6 highly pathogenic avian influenza viruses (HPAIVs) have been responsible for outbreaks in poultry and wild birds around Asia. H5N6 HPAIV is also a public concern due to sporadic human infections being reported in China. In the current study, we isolated an H5N6 HPAIV strain (A/Muscovy duck/Long An/AI470/2018; AI470) from an outbreak at a Muscovy duck farm in Long An Province in Southern Vietnam in July 2018 and genetically characterized it. Basic Local Alignment Search Tool (BLAST) analysis revealed that the eight genomic segments of AI470 were most closely related (99.6%–99.9%) to A/common gull/Saratov/1676/2018 (H5N6), which was isolated in October 2018 in Russia. Furthermore, AI470 also shared 99.4%–99.9% homology with A/Guangxi/32797/2018, an H5N6 HPAIV strain that infected humans in China in 2018. Phylogenetic analyses of the entire genome showed that AI470 was directly derived from H5N6 HPAIVs that were in South China from 2015 to 2018 and clustered with four H5N6 HPAIV strains of human origin in South China from 2017 to 2018. This indicated that AI470 was introduced into Vietnam from China. In addition, molecular characteristics related to mammalian adaptation among the recent human H5N6 HPAIV viruses, except PB2 E627K, were shared by AI470. These findings are cause for concern since H5N6 HPAIV strains that possess a risk of human infection have crossed the Chinese border. [ABSTRACT FROM AUTHOR]

Three viruses included in the study were isolated from dead birds (A/duck/Omsk/1822/2006, A/chicken/Reshoty/02/2006, and A/duck/Tuva/01/2006), whereas the virus A/common gull/Chany/P/2006 was isolated from an apparently healthy gull during outbreaks of highly pathogenic avian influenza in Russia in 2006. The intravenous pathogenicity index (IVPI) of viruses A/duck/Omsk/1822/2006, A/chicken/Reshoty/02/2006, and A/duck/Tuva/01/2006 ranged from 2.7 to 3.0, while the virus A/common gull/Chany/P/2006 had a markedly lower IVPI of 1.7. The virus A/common gull/Chany/P/2006 had a unique pattern of six amino acid substitutions in the regions of viral proteins crucial for virulence of H5N1 viruses. We hypothesize that these substitutions may affect the pathogenicity of A/common gull/Chany/P/2006. [ABSTRACT FROM AUTHOR]

Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in three different distinct geographic regions of Northern Eurasia and studied their characteristics. H12N2 from the Far East region was a double reassortant containing hemagglutinin (HA), non-structural (NS) and nucleoprotein (NP) segments of the American lineage and others from the classical Eurasian avian-like lineage. H12N5 viruses contain Eurasian lineage segments. We suggest a phylogeographical scheme for reassortment events associated with geographical groups of aquatic birds and their migration flyways. The H12N2 virus is of particular interest as this subtype has been found in common teal in the Russian Far East region, and it has a strong relation to North American avian influenza virus lineages, clearly showing that viral exchange of segments between the two continents does occur. Our results emphasize the importance of Avian Influenza Virus (AIV) surveillance in Northern Eurasia for the annual screening of virus characteristics, including the genetic constellation of rare virus subtypes, to understand the evolutionary ecology of AIV. [ABSTRACT FROM AUTHOR]

Avian orthoavulavirus 13 (AOAV-13), also named avian paramyxovirus 13 (APMV-13), has been found sporadically in wild birds around the world ever since the discovery of AOAV-13 (AOAV-13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV-13 in China. In the present study, a novel AOAV-13 virus (AOAV-13/wild goose/China/Hubei/V93-1/2015), isolated from a wild migratory waterfowl in a wetland of Hubei province of China, during active surveillance from 2013 to 2018, was biologically and genetically characterized. Phylogenetic analyses demonstrated a very close genetic relationship among all AOAV-13 strains, as revealed by very few genetic variations. Moreover, pathogenicity tests indicated that the V93-1 strain is a low virulent virus for chickens. However, the genome of the V93-1 virus was found to be 16,158 nucleotides (nt) in length, which is 12 nt or 162 nt longer than the other AOAV-13 strains that have been reported to date. The length difference of 12 nt in strain V93-1 is due to the existence of three repeats of the conserved sequence, "AAAAAT", in the 5′-end trailer of the genome. Moreover, the HN gene of the V93-1 virus is 2070 nt in size, encoding 610 aa, which is the same size as the AOAV-13 strain from Japan, whereas that of two strains from Ukraine and Kazakhstan are 2080 nt in length, encoding 579 aa. We describe a novel AOAV-13 in migratory waterfowl in China, which suggests that diversified trailer region sequences and HN gene lengths exist within serotype AOAV-13, and highlight the need for its constant surveillance in poultry from live animal markets, and especially migratory birds. [ABSTRACT FROM AUTHOR]